TotalSegmentator installation problem due to Zenodo connection error

I have some problems installing TotalSegmentator. Let me try to describe it clearly. I hope to get your help.
My device:DELL windows 10 NVIDIA GeForceRTX3060 ,Display Memory: 28386 MB

pyTorch :version 1.13+cu117
NVidia driver: version 512.77

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Processing started

Writing input file to C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2023-02-08_16+16+43.146/total-segmentator-input.nii

Creating segmentations with TotalSegmentator AI…

Total Segmentator arguments: [‘-i’, ‘C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2023-02-08_16+16+43.146/total-segmentator-input.nii’, ‘-o’, ‘C:/Users/Administrator/AppData/Local/Temp/Slicer/__SlicerTemp__2023-02-08_16+16+43.146/segmentation’, ‘–ml’, ‘–task’, ‘total’]

If you use this tool please cite: [2208.05868] TotalSegmentator: robust segmentation of 104 anatomical structures in CT images

Downloading pretrained weights for Task 251 (~230MB) …

Traceback (most recent call last):

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\urllib3\connection.py”, line 174, in _new_conn

conn = connection.create_connection(

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\urllib3\util\connection.py”, line 72, in create_connection

for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\socket.py”, line 954, in getaddrinfo

for res in _socket.getaddrinfo(host, port, family, type, proto, flags):

socket.gaierror: [Errno 11004] getaddrinfo failed

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\urllib3\connectionpool.py”, line 703, in urlopen

httplib_response = self._make_request(

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\urllib3\connectionpool.py”, line 386, in _make_request

self._validate_conn(conn)

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\urllib3\connectionpool.py”, line 1042, in _validate_conn

conn.connect()

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\urllib3\connection.py”, line 358, in connect

self.sock = conn = self._new_conn()

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\urllib3\connection.py”, line 186, in _new_conn

raise NewConnectionError(

urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x0000023943A0D700>: Failed to establish a new connection: [Errno 11004] getaddrinfo failed

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\requests\adapters.py”, line 489, in send

resp = conn.urlopen(

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\urllib3\connectionpool.py”, line 787, in urlopen

retries = retries.increment(

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\urllib3\util\retry.py”, line 592, in increment

raise MaxRetryError(_pool, url, error or ResponseError(cause))

urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host=‘zenodo.org’, port=443): Max retries exceeded with url: /record/6802342/files/Task251_TotalSegmentator_part1_organs_1139subj.zip?download=1 (Caused by NewConnectionError(‘<urllib3.connection.HTTPSConnection object at 0x0000023943A0D700>: Failed to establish a new connection: [Errno 11004] getaddrinfo failed’))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Scripts\TotalSegmentator”, line 241, in

main()

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Scripts\TotalSegmentator”, line 200, in main

download_pretrained_weights(tid)

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\totalsegmentator\libs.py”, line 175, in download_pretrained_weights

download_url_and_unpack(WEIGHTS_URL, config_dir)

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\totalsegmentator\libs.py”, line 69, in download_url_and_unpack

raise e

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\totalsegmentator\libs.py”, line 55, in download_url_and_unpack

with requests.get(url, stream=True) as r:

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\requests\api.py”, line 73, in get

return request(“get”, url, params=params, **kwargs)

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\requests\api.py”, line 59, in request

return session.request(method=method, url=url, **kwargs)

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\requests\sessions.py”, line 587, in request

resp = self.send(prep, **send_kwargs)

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\requests\sessions.py”, line 701, in send

r = adapter.send(request, **kwargs)

File “C:\ProgramData\NA-MIC\Slicer 5.2.1\lib\Python\Lib\site-packages\requests\adapters.py”, line 565, in send

raise ConnectionError(e, request=request)

requests.exceptions.ConnectionError: HTTPSConnectionPool(host=‘zenodo.org’, port=443): Max retries exceeded with url: /record/6802342/files/Task251_TotalSegmentator_part1_organs_1139subj.zip?download=1 (Caused by NewConnectionError(‘<urllib3.connection.HTTPSConnection object at 0x0000023943A0D700>: Failed to establish a new connection: [Errno 11004] getaddrinfo failed’))

It looks like the file download failed. I have gotten timeouts from zenodo.org before using a web browser so I’m sure the same thing would happen from time to time using the programatic interface too. Probably try again in a few hours or days when it’s less busy.

Thank you. It’s really unstable. I have tested many times and always failed, using VPN or not ,using different WiFi at different times. 3d_ The fullres folder is always empty.Is there any other way? For example, download some files manually.

1 Like

I was able to install TotalSegmentator yesterday on a new windows machine. It took a while but it succeeded. I don’t know if it matters where the connection comes from; in my experience it is the server just being overwhelmed from time to time. If this keeps up we might want to find a way to mirror the files somewhere else (google drive, github release, etc).

Yesterday our collaborators from Hungary reported Zenodo servers timing out, too.

@zhangliang could you please report this problem in the TotalSegmentator Python package repository? It is important for the developers to know about this issue and start thinking about alternative hosting options.

OK, I have submitted the problem as required, and I look forward to solving it.

I have met up with this problem too. may local weights added to slicer plugin, and upload the weights to google drive ?

Hello, I think I have solved this problem. You can manually download the zip file and put it in the specified location. You can sign in http://zenodo.org/ And search for missing files

1 Like

yes!!! I have download all this zip files manually, it worked

2 posts were split to a new topic: How to segment the tibia using TotalSegmentator?

C:\Users\XXX.totalsegmentator\nnunet\results\nnUNet\3d_fullres

and it works, thx!